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<h1 class="title toc-ignore">Enrichment results of triglycerides</h1>
<h4 class="author"><em>Xiang Zhu</em></h4>
<h4 class="date"><em>2017-04-12</em></h4>
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<p><strong>Last updated:</strong> 2018-07-02</p>
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<p><summary> <strong style="color:blue;">✔</strong> <strong>Repository version:</strong> <a href="https://github.com/xiangzhu/rss-gsea/tree/a1a2c02282e3af670d26fae43407cd3deb026549" target="_blank">a1a2c02</a> </summary></p>
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<div id="input-data" class="section level2">
<h2>Input data</h2>
<p>Results below were generated from the GWAS summary statistics published in the paper <a href="https://www.ncbi.nlm.nih.gov/pubmed/20686565">“Biological, Clinical and Population Relevance of 95 Loci for Blood Lipids” (<em>Nature</em>, 2010)</a>. The summary data file is available at <a href="http://csg.sph.umich.edu/willer/public/lipids2010" class="uri">http://csg.sph.umich.edu/willer/public/lipids2010</a>.</p>
</div>
<div id="analysis-results" class="section level2">
<h2>Analysis results</h2>
<p>Enrichment analyses are summarized by the following three quantities.</p>
<ul>
<li><strong>BF:</strong> Bayes factor comparing the enrichment model against the baseline model;</li>
<li><strong>Outside <span class="math inline">\(\pi\)</span>:</strong> proportion of trait-associated SNPs that are “outside” the gene set;</li>
<li><strong>Inside <span class="math inline">\(\pi\)</span>:</strong> proportion of trait-associated SNPs that are “inside” the gene set.</li>
</ul>
<p>The first quantity reflects the significance of enrichment, whereas the last two capture the magnitude of enrichment. For each gene set, we report these three quantities in the last three columns of tables below, on log 10 scale.</p>
<div id="biological-pathways" class="section level3">
<h3>Biological pathways</h3>
<div id="htmlwidget-983860bb2d7d6ad3a872" style="width:100%;height:auto;" class="datatables html-widget"></div>
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1<br/>(reactome, PC)","Metabolism of water-soluble vitamins and cofactors<br/>(reactome, BioSystems)","Biotin transport and metabolism<br/>(reactome, PC)","Transport of vitamins, nucleosides, and related molecules<br/>(reactome, PC)","Pyrimidine metabolism<br/>(kegg, BioSystems)","Vitamin B5 (pantothenate) metabolism<br/>(reactome, PC)","Unfolded Protein Response (UPR)<br/>(reactome, BioSystems)","XBP1(S) activates chaperone genes<br/>(reactome, PC)","XBP1(S) activates chaperone genes<br/>(reactome, BioSystems)","Nucleotide metabolism<br/>(reactome, PC)","Metabolism of nucleotides<br/>(reactome, BioSystems)","SLC-mediated transmembrane transport<br/>(reactome, PC)","SLC-mediated transmembrane transport<br/>(reactome, BioSystems)","Carbohydrate metabolism<br/>(reactome, PC)","Metabolism of carbohydrates<br/>(reactome, BioSystems)","Role of PI3K subunit p85 in regulation of Actin Organization and Cell Migration<br/>(biocarta, BioCarta)","How does salmonella hijack a cell<br/>(biocarta, BioCarta)","selenocysteine biosynthesis<br/>(humancyc, PC)","Electric Transmission Across Gap Junctions<br/>(reactome, PC)","Trafficking of dietary sterols<br/>(reactome, PC)","Rapid glucocorticoid signaling<br/>(pid, PC)"],[22,25,132,241,41,28,29,39,45,47,79,78,203,2,3,8,8,6,75,9,45,55,80,41,5,36,30,17,30,50,58,67,112,184,107,193,109,136,169,163,110,3,181,39,40,15,42,88,89,174,231,3,3,23,41,19,41,116,40,12,19,496,5,7,12,12,333,19,19,22,33,32,34,98,17,24,95,24,86,86,10,36,101,11,85,43,53,76,77,251,254,244,253,16,13,6,5,3,8],[1717,1937,5700,15090,3153,2120,2207,2999,3486,3640,5680,5680,11647,189,291,612,612,592,5975,666,3426,4043,6892,3561,455,3979,2313,1139,2617,3958,4462,6159,11606,14845,11201,15724,11300,6102,15637,14025,11507,261,17640,4540,4540,1460,3584,8916,8916,17080,19644,248,294,2340,4228,1506,2630,10356,4168,865,2337,46258,505,636,842,907,31611,1400,1465,2093,3661,3186,2765,8939,1295,2011,8540,2600,7949,7949,1069,3390,7983,722,6588,3296,3913,6964,6964,23440,23907,22581,23147,1109,865,486,489,203,751],[1354.14832171506,1352.72914990889,1214.6109225319,1188.0293841979,1054.65798681584,1044.19346795297,1044.12123140806,1043.51528936178,1043.23435069835,1043.15722675462,604.901482017045,455.672605413639,435.503195561107,398.767866831792,398.016514046411,397.474874548689,397.474874548689,396.848833294518,389.360477592351,388.8792256668,386.023481065543,385.951267408337,353.261151653257,346.024128924221,285.704129415691,224.746099657064,220.208532298874,210.278381475553,210.274327185105,197.885080751346,197.408557895235,150.079365563885,136.229171652122,135.651334755198,133.712477975593,132.98796154795,132.975996310409,131.268638491316,130.584692061207,128.929917728962,126.98274490922,124.894339289904,122.022542421239,121.471364459704,121.471364459704,117.004490348574,115.883942203255,114.441884634811,114.441884634811,109.281487850634,106.252923223794,102.511729140706,99.9232606378436,96.4968452156743,96.088298682389,94.1190779946292,90.5266330322301,89.7924440107434,88.7676869066282,88.6903869211066,88.6331134703308,76.2936934239488,72.3674321569454,40.6611907511952,40.1669506118169,39.1637518784599,23.6458310045812,22.3309339160373,20.7380113542722,20.6533346498989,19.4412423323418,19.2712063177029,19.1165090558207,18.3743054136943,15.9980053028471,15.7021095360743,14.3506954456633,13.1489939911002,10.6732597893993,10.6732597893993,10.6620579251764,10.569646292936,10.0118219144582,9.60069172850937,8.29480010847606,5.96156607481586,5.77720912997757,3.61702054440372,3.61702054440372,2.05913201419033,2.02935827281373,1.05938629443445,0.914174801502904,-0.036774946119329,-0.0402649048335161,-0.0702398274956992,-0.0723312138260821,-0.0784374051818246,-0.0848742722785657],["-4.3911<br/>[-4.3916, -4.3892]","-4.3910<br/>[-4.3915, -4.3891]","-4.3895<br/>[-4.3900, -4.3876]","-4.3856<br/>[-4.3860, -4.3836]","-4.4011<br/>[-4.4015, -4.3991]","-4.4015<br/>[-4.4019, -4.3995]","-4.4014<br/>[-4.4019, -4.3995]","-4.4011<br/>[-4.4015, -4.3991]","-4.4009<br/>[-4.4013, -4.3989]","-4.4008<br/>[-4.4013, -4.3989]","-4.3895<br/>[-4.3899, -4.3875]","-4.3895<br/>[-4.3899, -4.3875]","-4.3870<br/>[-4.3874, -4.3851]","-4.3617<br/>[-4.3621, -4.3599]","-4.3616<br/>[-4.3620, -4.3598]","-4.3615<br/>[-4.3619, -4.3597]","-4.3615<br/>[-4.3619, -4.3597]","-4.3615<br/>[-4.3619, -4.3597]","-4.3691<br/>[-4.3694, -4.3675]","-4.3615<br/>[-4.3619, -4.3597]","-4.3603<br/>[-4.3607, -4.3585]","-4.3601<br/>[-4.3605, -4.3583]","-4.3684<br/>[-4.3687, -4.3665]","-4.5091<br/>[-4.5096, -4.5065]","-4.3616<br/>[-4.3620, -4.3598]","-4.3601<br/>[-4.3605, -4.3583]","-4.5823<br/>[-4.5829, -4.5797]","-4.5531<br/>[-4.5537, -4.5505]","-4.5821<br/>[-4.5827, -4.5795]","-4.5815<br/>[-4.5821, -4.5790]","-4.5813<br/>[-4.5819, -4.5787]","-4.5358<br/>[-4.5364, -4.5332]","-4.4792<br/>[-4.4797, -4.4768]","-4.3655<br/>[-4.3659, -4.3637]","-4.4794<br/>[-4.4799, -4.4770]","-4.3651<br/>[-4.3655, -4.3633]","-4.4794<br/>[-4.4799, -4.4770]","-4.3894<br/>[-4.3898, -4.3874]","-4.4786<br/>[-4.4791, -4.4763]","-4.3657<br/>[-4.3660, -4.3641]","-4.4793<br/>[-4.4798, -4.4769]","-4.3617<br/>[-4.3620, -4.3598]","-4.4767<br/>[-4.4772, -4.4743]","-4.4702<br/>[-4.4707, -4.4680]","-4.4702<br/>[-4.4707, -4.4680]","-4.4577<br/>[-4.4582, -4.4557]","-4.5091<br/>[-4.5096, -4.5065]","-4.4684<br/>[-4.4689, -4.4661]","-4.4684<br/>[-4.4689, -4.4661]","-4.4769<br/>[-4.4775, -4.4746]","-4.4280<br/>[-4.4285, -4.4260]","-4.3617<br/>[-4.3621, -4.3599]","-4.3616<br/>[-4.3620, -4.3598]","-4.4233<br/>[-4.4238, -4.4213]","-4.4230<br/>[-4.4234, -4.4209]","-4.4240<br/>[-4.4244, -4.4219]","-4.4232<br/>[-4.4236, -4.4211]","-4.3669<br/>[-4.3673, -4.3651]","-4.4230<br/>[-4.4234, -4.4210]","-4.4128<br/>[-4.4133, -4.4108]","-4.4237<br/>[-4.4242, -4.4217]","-4.4233<br/>[-4.4236, -4.4218]","-4.4130<br/>[-4.4135, -4.4110]","-4.3615<br/>[-4.3619, -4.3597]","-4.3614<br/>[-4.3618, -4.3596]","-4.3614<br/>[-4.3618, -4.3596]","-4.3781<br/>[-4.3785, -4.3762]","-4.3612<br/>[-4.3616, -4.3594]","-4.3612<br/>[-4.3615, -4.3593]","-4.3609<br/>[-4.3613, -4.3591]","-4.3602<br/>[-4.3606, -4.3584]","-4.3604<br/>[-4.3608, -4.3586]","-4.3606<br/>[-4.3610, -4.3588]","-4.3581<br/>[-4.3585, -4.3563]","-4.3612<br/>[-4.3616, -4.3594]","-4.3609<br/>[-4.3613, -4.3591]","-4.3583<br/>[-4.3586, -4.3565]","-4.3607<br/>[-4.3611, -4.3589]","-4.3584<br/>[-4.3588, -4.3566]","-4.3584<br/>[-4.3588, -4.3566]","-4.3614<br/>[-4.3618, -4.3596]","-4.3603<br/>[-4.3607, -4.3585]","-4.3584<br/>[-4.3588, -4.3566]","-4.3615<br/>[-4.3619, -4.3597]","-4.3688<br/>[-4.3692, -4.3673]","-4.3604<br/>[-4.3608, -4.3586]","-4.3601<br/>[-4.3605, -4.3583]","-4.3588<br/>[-4.3592, -4.3570]","-4.3588<br/>[-4.3592, -4.3570]","-4.4025<br/>[-4.4029, -4.4006]","-4.4023<br/>[-4.4027, -4.4004]","-4.4035<br/>[-4.4040, -4.4015]","-4.4033<br/>[-4.4037, -4.4013]","-4.3613<br/>[-4.3617, -4.3595]","-4.3614<br/>[-4.3618, -4.3596]","-4.3616<br/>[-4.3620, -4.3598]","-4.3616<br/>[-4.3620, -4.3598]","-4.3617<br/>[-4.3621, -4.3599]","-4.3615<br/>[-4.3618, -4.3596]"],["-2.1620<br/>[-2.2347, -2.1552]","-2.2871<br/>[-2.2871, -2.2870]","-2.7968<br/>[-2.7969, -2.7965]","-3.2177<br/>[-3.2177, -3.2177]","-2.7204<br/>[-2.7205, -2.7203]","-2.6272<br/>[-2.6273, -2.6270]","-2.6446<br/>[-2.6448, -2.6445]","-2.7779<br/>[-2.7779, -2.7778]","-2.8432<br/>[-2.8433, -2.8431]","-2.8620<br/>[-2.8621, -2.8619]","-2.6080<br/>[-2.6080, -2.6080]","-2.7950<br/>[-2.8205, -2.7121]","-3.1116<br/>[-3.1116, -3.1115]","-1.6533<br/>[-1.6742, -1.5746]","-1.8330<br/>[-1.8570, -1.7311]","-2.1705<br/>[-2.1828, -2.1570]","-2.1705<br/>[-2.1828, -2.1570]","-2.1578<br/>[-2.1678, -2.1457]","-2.9902<br/>[-2.9982, -2.9834]","-2.2197<br/>[-2.2213, -2.2175]","-2.9217<br/>[-2.9300, -2.9121]","-2.9949<br/>[-3.0025, -2.9873]","-2.9309<br/>[-2.9334, -2.9288]","-2.2937<br/>[-2.2937, -2.2937]","-2.0510<br/>[-2.0548, -2.0460]","-2.3405<br/>[-2.3435, -2.3399]","-1.6370<br/>[-1.6387, -1.6368]","-1.4065<br/>[-1.4088, -1.3943]","-1.6905<br/>[-1.6994, -1.6738]","-1.8531<br/>[-1.8543, -1.8421]","-1.9001<br/>[-1.9001, -1.9000]","-2.0363<br/>[-2.0363, -2.0276]","-2.6073<br/>[-2.6074, -2.6073]","-2.4996<br/>[-2.4997, -2.4966]","-2.5552<br/>[-2.5669, -2.5552]","-2.5039<br/>[-2.5039, -2.5038]","-2.6107<br/>[-2.6113, -2.6031]","-2.9398<br/>[-2.9399, -2.9398]","-2.6428<br/>[-2.7218, -2.6291]","-3.0135<br/>[-3.0139, -3.0131]","-2.6783<br/>[-2.6783, -2.6704]","-2.1091<br/>[-2.1154, -2.0990]","-2.8193<br/>[-2.8259, -2.8119]","-2.2073<br/>[-2.2376, -2.1876]","-2.2073<br/>[-2.2376, -2.1876]","-1.7411<br/>[-1.7576, -1.7390]","-2.1711<br/>[-2.2293, -2.1711]","-2.5094<br/>[-2.5303, -2.4854]","-2.5094<br/>[-2.5303, -2.4854]","-2.8819<br/>[-2.9034, -2.8601]","-2.8006<br/>[-2.8045, -2.7940]","-1.8773<br/>[-1.9112, -1.8312]","-2.1590<br/>[-2.1670, -2.1458]","-2.1571<br/>[-2.1626, -2.1518]","-2.3330<br/>[-2.3332, -2.3329]","-1.7919<br/>[-1.7928, -1.7919]","-2.2735<br/>[-2.3042, -2.2449]","-2.2978<br/>[-2.3010, -2.2958]","-2.2809<br/>[-2.2938, -2.2765]","-1.6911<br/>[-1.6911, -1.6856]","-2.1044<br/>[-2.1156, -2.0974]","-3.2524<br/>[-3.2590, -3.2432]","-1.6004<br/>[-1.6077, -1.5906]","-2.0978<br/>[-2.1010, -2.0959]","-2.1307<br/>[-2.2040, -2.0733]","-2.2361<br/>[-2.2426, -2.2296]","-3.4775<br/>[-3.5652, -3.4020]","-2.5352<br/>[-2.5383, -2.5328]","-2.5580<br/>[-2.5612, -2.5559]","-2.7148<br/>[-2.7170, -2.7133]","-2.9532<br/>[-2.9572, -2.9510]","-2.8879<br/>[-2.9931, -2.8879]","-2.8347<br/>[-2.9497, -2.8347]","-2.9770<br/>[-2.9770, -2.9740]","-2.5751<br/>[-2.5977, -2.5637]","-2.7681<br/>[-2.7892, -2.7558]","-3.0155<br/>[-3.0341, -2.9825]","-2.7600<br/>[-2.7822, -2.7468]","-3.3841<br/>[-3.4003, -3.3731]","-3.3841<br/>[-3.4003, -3.3731]","-2.5248<br/>[-2.5403, -2.5162]","-3.0524<br/>[-3.0529, -3.0520]","-3.2814<br/>[-3.2893, -3.2757]","-2.3815<br/>[-2.3817, -2.3813]","-3.1628<br/>[-3.1746, -3.1227]","-3.0179<br/>[-3.0302, -3.0081]","-3.0939<br/>[-3.1074, -3.0855]","-3.5163<br/>[-3.5335, -3.5045]","-3.5163<br/>[-3.5335, -3.5045]","-3.4657<br/>[-3.4672, -3.4645]","-3.4743<br/>[-3.4757, -3.4731]","-3.5774<br/>[-3.5786, -3.5767]","-3.5884<br/>[-3.5900, -3.5878]","-5.9220<br/>[-8.1068, -5.1913]","-5.8599<br/>[-8.1837, -5.1086]","-4.9315<br/>[-7.6959, -4.1815]","-5.4335<br/>[-8.2374, -4.6909]","-4.3762<br/>[-7.5222, -3.6258]","-5.4773<br/>[-8.1410, -4.7592]"]],"container":"<table class=\"white-space: nowrap\">\n <thead>\n <tr>\n <th>Pathway name<br/>(database, repository)<\/th>\n <th># of genes<\/th>\n <th># of SNPs<\/th>\n <th>Log10 BF<\/th>\n <th>Log10 outside π<br/>(mean, 95% CI)<\/th>\n <th>Log10 inside π<br/>(mean, 95% CI)<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2,3]}],"order":[],"autoWidth":false,"orderClasses":false,"rowCallback":"function(row, data) {\nDTWidget.formatRound(this, row, data, 3, 3, 3, ',', '.');\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
</div>
<div id="tissue-highly-expressed-genes" class="section level3">
<h3>Tissue highly expressed genes</h3>
<div id="htmlwidget-0aaad034f4771159c3b9" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-0aaad034f4771159c3b9">{"x":{"filter":"none","data":[["Liver","Small Intestine - Terminal Ileum","Testis","Adrenal Gland","Colon - Transverse","Stomach","Esophagus - Gastroesophageal Junction","Prostate","Esophagus - Muscularis","Artery - Coronary","Artery - Aorta","Brain - Cortex","Brain - Anterior cingulate cortex (BA24)","Brain - Frontal Cortex (BA9)","Brain - Hippocampus","Brain - Nucleus accumbens (basal ganglia)","Brain - Hypothalamus","Brain - Caudate (basal ganglia)","Brain - Putamen (basal ganglia)","Uterus","Colon - Sigmoid","Artery - Tibial","Brain - Cerebellum","Muscle - Skeletal","Spleen","Cells - EBV-transformed lymphocytes","Thyroid","Lung","Heart - Left Ventricle","Heart - Atrial Appendage","Breast - Mammary Tissue","Adipose - Visceral (Omentum)","Nerve - Tibial","Whole Blood","Pituitary","Cells - Transformed fibroblasts","Brain - Cerebellar Hemisphere","Pancreas","Skin - Not Sun Exposed (Suprapubic)","Adipose - Subcutaneous","Skin - Sun Exposed (Lower leg)","Vagina","Esophagus - Mucosa","Ovary"],[6031,4469,5546,5351,4956,5002,5523,5308,5713,5882,6051,5539,5625,5908,5477,5828,5628,6191,6258,5397,5621,5762,5377,5339,3832,4731,5875,4766,5328,5537,5296,5548,5409,5594,5606,5827,5356,4867,5479,5357,5418,5495,5337,5586],[93.1542119159333,83.1863645830301,79.6243039614252,13.4085949967055,10.5741345050047,10.5677766497143,10.5060250118604,10.4437416424542,10.4270658775884,10.3522859400102,10.2888855818954,9.88509186517713,9.58986411453806,9.5835485088348,9.55851362082045,8.90752937228705,8.81207585757178,8.66883077669917,8.637981410632,8.29965214982896,8.24262898197752,8.21138311559068,7.54644711659432,7.03975742582025,3.4591285762185,3.32233387902677,3.31195647711782,3.22009718147552,3.2176309879305,3.20645715804936,3.16374866800773,3.12828327358209,3.10192582945574,3.0844947318856,3.06083260353972,2.9959216752157,1.77309998861885,1.59657648790071,1.58195209732811,1.57782848683228,1.56320147758131,1.5407407375607,1.53997293783105,1.53110039472676],["-4.4334<br/>[-4.4339, -4.4313]","-4.4223<br/>[-4.4228, -4.4202]","-4.4219<br/>[-4.4223, -4.4198]","-4.3794<br/>[-4.3798, -4.3776]","-4.3795<br/>[-4.3799, -4.3776]","-4.3795<br/>[-4.3799, -4.3776]","-4.3793<br/>[-4.3797, -4.3774]","-4.3794<br/>[-4.3798, -4.3775]","-4.3792<br/>[-4.3796, -4.3773]","-4.3791<br/>[-4.3795, -4.3772]","-4.3790<br/>[-4.3795, -4.3772]","-4.3703<br/>[-4.3707, -4.3687]","-4.3703<br/>[-4.3707, -4.3687]","-4.3702<br/>[-4.3705, -4.3686]","-4.3704<br/>[-4.3707, -4.3688]","-4.3695<br/>[-4.3699, -4.3677]","-4.3696<br/>[-4.3699, -4.3678]","-4.3693<br/>[-4.3697, -4.3675]","-4.3693<br/>[-4.3697, -4.3675]","-4.3793<br/>[-4.3797, -4.3774]","-4.3792<br/>[-4.3796, -4.3773]","-4.3792<br/>[-4.3796, -4.3773]","-4.3697<br/>[-4.3701, -4.3679]","-4.3691<br/>[-4.3695, -4.3673]","-4.3602<br/>[-4.3605, -4.3583]","-4.3598<br/>[-4.3602, -4.3580]","-4.3593<br/>[-4.3597, -4.3575]","-4.3598<br/>[-4.3601, -4.3579]","-4.3595<br/>[-4.3599, -4.3577]","-4.3594<br/>[-4.3598, -4.3576]","-4.3595<br/>[-4.3599, -4.3577]","-4.3594<br/>[-4.3598, -4.3576]","-4.3595<br/>[-4.3599, -4.3577]","-4.3594<br/>[-4.3598, -4.3576]","-4.3594<br/>[-4.3598, -4.3576]","-4.3593<br/>[-4.3597, -4.3575]","-4.3595<br/>[-4.3599, -4.3577]","-4.3597<br/>[-4.3601, -4.3579]","-4.3595<br/>[-4.3598, -4.3576]","-4.3595<br/>[-4.3599, -4.3577]","-4.3595<br/>[-4.3599, -4.3577]","-4.3594<br/>[-4.3598, -4.3576]","-4.3595<br/>[-4.3599, -4.3577]","-4.3594<br/>[-4.3598, -4.3576]"],["-2.4642<br/>[-2.5060, -2.4273]","-2.4594<br/>[-2.4844, -2.4371]","-2.6301<br/>[-2.6383, -2.6286]","-2.7398<br/>[-2.8305, -2.6600]","-2.9719<br/>[-3.0385, -2.9086]","-2.9748<br/>[-3.0419, -2.9100]","-2.9966<br/>[-3.0760, -2.9204]","-3.0053<br/>[-3.0715, -2.9413]","-3.0136<br/>[-3.0928, -2.9370]","-3.0329<br/>[-3.1172, -2.9632]","-3.0479<br/>[-3.1256, -2.9735]","-2.8057<br/>[-2.9258, -2.7173]","-2.8430<br/>[-2.9434, -2.7548]","-2.8543<br/>[-2.9601, -2.7653]","-2.8451<br/>[-2.9388, -2.7614]","-3.0006<br/>[-3.1000, -2.9087]","-2.8668<br/>[-2.9715, -2.7904]","-2.8964<br/>[-3.0021, -2.8107]","-2.9021<br/>[-3.0063, -2.8144]","-3.1059<br/>[-3.2166, -3.0102]","-3.1241<br/>[-3.2394, -3.0278]","-3.1363<br/>[-3.2529, -3.0450]","-2.8141<br/>[-2.9494, -2.7206]","-3.1176<br/>[-3.2266, -3.0261]","-3.1441<br/>[-3.2909, -3.0251]","-3.2232<br/>[-3.3857, -3.0965]","-3.2588<br/>[-3.4669, -3.1113]","-3.2528<br/>[-3.3947, -3.1290]","-3.2662<br/>[-3.4449, -3.1227]","-3.2706<br/>[-3.4602, -3.1136]","-3.2835<br/>[-3.4527, -3.1475]","-3.3013<br/>[-3.4771, -3.1653]","-3.3096<br/>[-3.4612, -3.1820]","-3.3202<br/>[-3.4712, -3.1821]","-3.3333<br/>[-3.4752, -3.2125]","-3.3655<br/>[-3.4911, -3.2507]","-3.4756<br/>[-3.7397, -3.2303]","-3.5776<br/>[-3.7151, -3.4062]","-3.5929<br/>[-3.7795, -3.3831]","-3.5937<br/>[-3.7676, -3.3922]","-3.6098<br/>[-3.7785, -3.4203]","-3.6278<br/>[-3.7868, -3.4492]","-3.6318<br/>[-3.7645, -3.4740]","-3.6387<br/>[-3.7808, -3.4605]"]],"container":"<table class=\"white-space: nowrap\">\n <thead>\n <tr>\n <th>Tissue name<\/th>\n <th># of SNPs<\/th>\n <th>Log10 BF<\/th>\n <th>Log10 outside π<br/>(mean, 95% CI)<\/th>\n <th>Log10 inside π<br/>(mean, 95% CI)<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2]}],"order":[],"autoWidth":false,"orderClasses":false,"rowCallback":"function(row, data) {\nDTWidget.formatRound(this, row, data, 2, 3, 3, ',', '.');\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
</div>
<div id="tissue-selectively-expressed-genes" class="section level3">
<h3>Tissue selectively expressed genes</h3>
<div id="htmlwidget-9dd0ac780160f191cf9f" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-9dd0ac780160f191cf9f">{"x":{"filter":"none","data":[["Testis","Heart_Left_Ventricle","Uterus","Ovary","Liver","Small_Intestine_Terminal_Ileum","Nerve_Tibial","Adipose_Subcutaneous","Adipose_Visceral_(Omentum)","Breast_Mammary_Tissue","Adrenal_Gland","Brain_Hippocampus","Brain_Nucleus_accumbens_(basal_ganglia)","Brain_Cortex","Brain_Anterior_cingulate_cortex_(BA24)","Brain_Caudate_(basal_ganglia)","Brain_Frontal_Cortex_(BA9)","Artery_Coronary","Colon_Sigmoid","Brain_Hypothalamus","Artery_Tibial","Artery_Aorta","Esophagus_Gastroesophageal_Junction","Esophagus_Muscularis","Muscle_Skeletal","Brain_Amygdala","Brain_Putamen_(basal_ganglia)","Kidney_Cortex","Brain_Cerebellum","Spleen","Whole_Blood","Brain_Cerebellar_Hemisphere","Brain_Substantia_nigra","Stomach","Skin_Sun_Exposed_(Lower_leg)","Skin_Not_Sun_Exposed_(Suprapubic)","Vagina","Esophagus_Mucosa","Pancreas","Colon_Transverse","Cells_EBV-transformed_lymphocytes","Lung","Minor_Salivary_Gland","Prostate","Pituitary","Cells_Transformed_fibroblasts","Heart_Atrial_Appendage","Thyroid","Brain_Spinal_cord_(cervical_c-1)"],[7341,10523,12002,11089,7791,8307,11948,9690,9380,9385,11749,10469,10876,11456,12462,11198,13138,11885,10503,11700,12067,13734,13552,13727,8241,10737,11273,8533,10443,6814,6765,13046,12199,8833,6457,6541,6402,6504,7318,7128,7421,7937,7991,8692,9091,10323,10619,11517,12173],[1085.74157813016,398.525002504387,390.661516036885,383.983863898373,142.443597174372,74.4661779038417,23.0603397838708,20.5001016598199,20.3905497167403,20.1229363463325,14.8417373285493,11.9587364794078,11.6477404063805,11.2975447414785,6.21224410884357,6.10916000396273,5.89266038830198,4.10618964594032,4.04837016949801,3.96637389741265,3.94156287868286,3.8765288125518,3.8555296398219,3.84300162035074,3.25656382640811,3.22027548881258,3.0167915962841,2.72236264463621,1.85035701895291,1.69982625851544,1.56342228687157,1.5189753227005,1.31219390677862,-0.0576112030531358,-0.354603240149886,-0.355487693059541,-0.356184105572825,-0.356212192177874,-0.363311615442401,-0.36355802348744,-0.364940436065734,-0.37435790418516,-0.374629341117649,-0.381902826759332,-0.384767926635826,-0.397645195941106,-0.397992150391013,-0.406534110680096,-0.411337184576539],["-4.3993<br/>[-4.3997, -4.3973]","-4.3573<br/>[-4.3577, -4.3555]","-4.3968<br/>[-4.3972, -4.3949]","-4.3571<br/>[-4.3575, -4.3553]","-4.4823<br/>[-4.4828, -4.4802]","-4.4207<br/>[-4.4211, -4.4186]","-4.3876<br/>[-4.3880, -4.3859]","-4.3878<br/>[-4.3882, -4.3859]","-4.3879<br/>[-4.3883, -4.3860]","-4.3879<br/>[-4.3883, -4.3860]","-4.3670<br/>[-4.3674, -4.3652]","-4.3679<br/>[-4.3682, -4.3662]","-4.3677<br/>[-4.3681, -4.3661]","-4.3675<br/>[-4.3678, -4.3658]","-4.3670<br/>[-4.3674, -4.3654]","-4.3676<br/>[-4.3679, -4.3659]","-4.3667<br/>[-4.3671, -4.3651]","-4.3766<br/>[-4.3770, -4.3747]","-4.3772<br/>[-4.3776, -4.3753]","-4.3666<br/>[-4.3670, -4.3648]","-4.3765<br/>[-4.3769, -4.3746]","-4.3758<br/>[-4.3762, -4.3739]","-4.3759<br/>[-4.3763, -4.3740]","-4.3758<br/>[-4.3762, -4.3739]","-4.3679<br/>[-4.3683, -4.3660]","-4.3678<br/>[-4.3681, -4.3661]","-4.3675<br/>[-4.3679, -4.3659]","-4.3745<br/>[-4.3748, -4.3730]","-4.3574<br/>[-4.3578, -4.3556]","-4.3589<br/>[-4.3593, -4.3571]","-4.3589<br/>[-4.3593, -4.3571]","-4.3562<br/>[-4.3566, -4.3544]","-4.3664<br/>[-4.3668, -4.3645]","-4.3584<br/>[-4.3588, -4.3566]","-4.3590<br/>[-4.3594, -4.3572]","-4.3590<br/>[-4.3594, -4.3572]","-4.3591<br/>[-4.3595, -4.3573]","-4.3590<br/>[-4.3594, -4.3572]","-4.3587<br/>[-4.3591, -4.3569]","-4.3588<br/>[-4.3591, -4.3569]","-4.3586<br/>[-4.3590, -4.3568]","-4.3584<br/>[-4.3588, -4.3566]","-4.3584<br/>[-4.3588, -4.3566]","-4.3581<br/>[-4.3585, -4.3563]","-4.3579<br/>[-4.3583, -4.3561]","-4.3574<br/>[-4.3578, -4.3556]","-4.3573<br/>[-4.3577, -4.3555]","-4.3569<br/>[-4.3573, -4.3551]","-4.3566<br/>[-4.3570, -4.3548]"],["-3.0206<br/>[-3.0206, -3.0206]","-3.1711<br/>[-3.1757, -3.1663]","-3.1730<br/>[-3.1754, -3.1717]","-3.4328<br/>[-3.4414, -3.4245]","-2.1907<br/>[-2.1909, -2.1886]","-2.8644<br/>[-2.8797, -2.8386]","-3.3230<br/>[-3.3813, -3.2637]","-3.3803<br/>[-3.4938, -3.2528]","-3.3822<br/>[-3.4865, -3.2678]","-3.4618<br/>[-3.4926, -3.4179]","-3.1875<br/>[-3.2621, -3.1233]","-3.4556<br/>[-3.4738, -3.4222]","-3.3809<br/>[-3.3969, -3.3466]","-3.3945<br/>[-3.4114, -3.3630]","-3.5216<br/>[-3.6130, -3.4473]","-3.5403<br/>[-3.5762, -3.5027]","-3.6180<br/>[-3.6472, -3.5846]","-3.6946<br/>[-3.7670, -3.5999]","-3.6954<br/>[-3.7192, -3.6566]","-3.7412<br/>[-3.7662, -3.6991]","-3.7522<br/>[-3.7796, -3.7073]","-3.7880<br/>[-3.8357, -3.7224]","-3.7982<br/>[-3.8305, -3.7568]","-3.8035<br/>[-3.8356, -3.7616]","-3.5178<br/>[-3.6241, -3.4100]","-3.6376<br/>[-3.7513, -3.5409]","-3.7301<br/>[-3.7755, -3.6809]","-3.5861<br/>[-3.6441, -3.5269]","-3.7254<br/>[-3.9987, -3.5508]","-3.7266<br/>[-3.8325, -3.5603]","-3.8096<br/>[-3.8302, -3.7638]","-3.9435<br/>[-4.1123, -3.8055]","-4.0612<br/>[-4.0862, -4.0053]","-4.1759<br/>[-5.3405, -3.8695]","-5.8878<br/>[-7.8051, -5.2106]","-5.8680<br/>[-7.7847, -5.1868]","-6.3048<br/>[-8.2564, -5.6262]","-6.0189<br/>[-7.9614, -5.3378]","-5.7831<br/>[-7.5747, -5.1133]","-5.9900<br/>[-7.9040, -5.3210]","-5.8008<br/>[-7.6554, -5.1177]","-6.3270<br/>[-8.2010, -5.6511]","-6.2550<br/>[-8.1173, -5.5733]","-6.2560<br/>[-8.1013, -5.5901]","-6.0901<br/>[-7.8998, -5.4081]","-6.3801<br/>[-8.1665, -5.7096]","-6.0438<br/>[-7.8129, -5.3693]","-6.2216<br/>[-7.9130, -5.5510]","-6.1696<br/>[-7.8918, -5.5062]"]],"container":"<table class=\"white-space: nowrap\">\n <thead>\n <tr>\n <th>Tissue name<\/th>\n <th># of SNPs<\/th>\n <th>Log10 BF<\/th>\n <th>Log10 outside π<br/>(mean, 95% CI)<\/th>\n <th>Log10 inside π<br/>(mean, 95% CI)<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2]}],"order":[],"autoWidth":false,"orderClasses":false,"rowCallback":"function(row, data) {\nDTWidget.formatRound(this, row, data, 2, 3, 3, ',', '.');\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
</div>
<div id="cluster-distinctively-expressed-genes" class="section level3">
<h3>Cluster distinctively expressed genes</h3>
<div id="htmlwidget-798b325e8770e69abc2e" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-798b325e8770e69abc2e">{"x":{"filter":"none","data":[["20","6","3","10","18","13","7","5","17","9","1","19","2","4","8","11","12","15","14","16"],[7633,8299,9528,7838,6874,7144,7741,10908,7943,9058,6991,5541,8397,11749,9664,9832,6806,7264,8906,9717],[90.8107250572076,54.8109804451901,23.9068781610282,17.9944715599469,6.30646307653262,5.37750963034239,4.88515594618289,4.20261819363374,2.85145078852127,2.81066737244041,2.47279864721555,1.41842298520542,1.28746085469105,0.832875305876417,0.29575606325425,0.0923936579318305,-0.405972382806272,-0.423291265816027,-0.432638055033061,-0.436571282735988],["-4.4327<br/>[-4.4332, -4.4307]","-4.3583<br/>[-4.3586, -4.3564]","-4.3981<br/>[-4.3985, -4.3961]","-4.3781<br/>[-4.3785, -4.3763]","-4.3882<br/>[-4.3886, -4.3864]","-4.3786<br/>[-4.3790, -4.3767]","-4.3681<br/>[-4.3685, -4.3662]","-4.3770<br/>[-4.3774, -4.3751]","-4.3592<br/>[-4.3595, -4.3575]","-4.3682<br/>[-4.3686, -4.3663]","-4.3588<br/>[-4.3592, -4.3570]","-4.3594<br/>[-4.3598, -4.3576]","-4.3590<br/>[-4.3593, -4.3574]","-4.3568<br/>[-4.3572, -4.3550]","-4.3577<br/>[-4.3581, -4.3559]","-4.3584<br/>[-4.3587, -4.3567]","-4.3589<br/>[-4.3593, -4.3571]","-4.3587<br/>[-4.3591, -4.3569]","-4.3580<br/>[-4.3584, -4.3562]","-4.3577<br/>[-4.3581, -4.3559]"],["-2.6487<br/>[-2.6870, -2.6118]","-2.9808<br/>[-2.9835, -2.9705]","-3.2550<br/>[-3.3540, -3.1576]","-2.9112<br/>[-2.9933, -2.8422]","-2.9762<br/>[-3.0496, -2.9112]","-3.3580<br/>[-3.3765, -3.2898]","-3.3840<br/>[-3.4223, -3.3356]","-3.6129<br/>[-3.7309, -3.4942]","-3.5781<br/>[-3.6355, -3.5137]","-3.5088<br/>[-3.6785, -3.3930]","-3.4088<br/>[-3.6960, -3.2717]","-3.6917<br/>[-3.7832, -3.5797]","-3.4520<br/>[-3.9400, -3.2383]","-3.7091<br/>[-3.7681, -3.6299]","-3.9930<br/>[-5.1910, -3.8057]","-4.0807<br/>[-5.0112, -3.8945]","-5.3253<br/>[-7.2605, -4.6328]","-6.2665<br/>[-8.1721, -5.5961]","-5.5726<br/>[-7.3870, -4.8895]","-5.5194<br/>[-7.1328, -4.8706]"]],"container":"<table class=\"white-space: nowrap\">\n <thead>\n <tr>\n <th>Cluster ID<\/th>\n <th># of SNPs<\/th>\n <th>Log10 BF<\/th>\n <th>Log10 outside π<br/>(mean, 95% CI)<\/th>\n <th>Log10 inside π<br/>(mean, 95% CI)<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[1,2]}],"order":[],"autoWidth":false,"orderClasses":false,"rowCallback":"function(row, data) {\nDTWidget.formatRound(this, row, data, 2, 3, 3, ',', '.');\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
<p>The relationship between tissues and clusters is shown in Figure 1 of <a href="http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006599">Dey et al. (2017)</a>; see below.</p>
<p><img src="http://journals.plos.org/plosgenetics/article/figure/image?size=large&id=10.1371/journal.pgen.1006599.g001" /></p>
</div>
</div>
<div id="session-information" class="section level2">
<h2>Session information</h2>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">sessionInfo</span>()</a></code></pre></div>
<pre><code>R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DT_0.4 plyr_1.8.4 dplyr_0.7.5 R.matlab_3.6.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.17 compiler_3.5.0 pillar_1.2.3
[4] later_0.7.3 git2r_0.21.0 workflowr_1.0.1
[7] bindr_0.1.1 R.methodsS3_1.7.1 R.utils_2.6.0
[10] tools_3.5.0 digest_0.6.15 jsonlite_1.5
[13] evaluate_0.10.1 tibble_1.4.2 pkgconfig_2.0.1
[16] rlang_0.2.1 shiny_1.1.0 crosstalk_1.0.0
[19] yaml_2.1.19 bindrcpp_0.2.2 stringr_1.3.1
[22] knitr_1.20 htmlwidgets_1.2 rprojroot_1.3-2
[25] tidyselect_0.2.4 glue_1.2.0 R6_2.2.2
[28] rmarkdown_1.10 purrr_0.2.5 magrittr_1.5
[31] whisker_0.3-2 backports_1.1.2 promises_1.0.1
[34] htmltools_0.3.6 assertthat_0.2.0 mime_0.5
[37] xtable_1.8-2 httpuv_1.4.4.1 stringi_1.2.3
[40] R.oo_1.22.0 </code></pre>
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